The man, in his 60s, was said to have suffered severe head injuries after he slipped while climbing down a ladder as the east London site was engulfed in torrential rain and lightning.
However a post-mortem examination revealed he suffered a fatal cardiac arrest, meaning no further action will be taken by Health and Safety Executive investigators as it is not a work-related death, a HSE spokesman said.
His body was found slumped in the crane’s stairwell. It was the second fatality among workers building the Olympic facilities after another had a non-work-related heart attack in 2009.
A London Ambulance Service spokesman added: 'We were called just after 2.30pm to Leyton Road, Stratford, where a man in a crane was in cardiac arrest and had stopped breathing.
'We sent three ambulance crews, a single responder in a car, and a doctor from the air ambulance, who went in a car.
'Sadly, the patient was pronounced dead by the doctor.'